Variant report

Variant	rs11770543
Chromosome Location	chr7:47700779-47700780
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:47690491..47692702-chr7:47700621..47703207,2	MCF-7	breast:

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10951916	0.80[CEU][hapmap];0.80[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs11766347	1.00[CEU][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12531737	0.80[CEU][hapmap];0.87[GIH][hapmap];0.84[MEX][hapmap]
rs12537656	0.80[CEU][hapmap];0.83[GIH][hapmap]
rs13242997	0.80[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap]
rs35341430	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4724608	0.80[CEU][hapmap];0.80[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs4724610	0.80[CEU][hapmap];0.80[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs6967317	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6969715	0.80[CEU][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs7790431	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7790476	1.00[CEU][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs965924	0.80[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026223	chr7:47560728-48243287	Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv888003	chr7:47694270-47907214	Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11770543	PKD1L1	cis	cerebellum	SCAN
rs11770543	CDC14C	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:47694600-47700800	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr7:47695000-47711000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr7:47696800-47701600	Enhancers	A549	lung
4	chr7:47698400-47704200	Weak transcription	HepG2	liver
5	chr7:47699000-47700800	Weak transcription	HSMMtube	muscle
6	chr7:47699200-47701000	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr7:47699600-47700800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr7:47699600-47700800	Weak transcription	Fetal Muscle Leg	muscle
9	chr7:47699800-47700800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr7:47699800-47705800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr7:47699800-47706000	Weak transcription	Pancreas	Pancrea
12	chr7:47700000-47700800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr7:47700000-47700800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr7:47700000-47708800	Weak transcription	Spleen	Spleen
15	chr7:47700600-47701200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr7:47700600-47701200	Enhancers	HMEC	breast
17	chr7:47700600-47701600	Enhancers	Fetal Kidney	kidney
18	chr7:47700600-47701800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr7:47700600-47701800	Enhancers	Primary B cells from cord blood	blood
20	chr7:47700600-47701800	Enhancers	Primary B cells from peripheral blood	blood
21	chr7:47700600-47701800	Enhancers	GM12878-XiMat	blood
22	chr7:47700600-47703400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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